Jake can hardly believe his eyes when his father introduces him to a woman who looks, talks and acts exactly like his late mother, Jennifer. She and Sisko reveal that this is Jennifer — at least, her double from a mirror universe which Sisko once visited, where she was married to his now-dead counterpart. Sisko leaves the two of them alone for awhile. But when he returns, Jennifer and Jake are nowhere to be found. All that remains is a small device, which Sisko realizes is used for transport to the mirror universe. He activates it and appears on Terok Nor, the other universe's Deep Space Nine, where he meets O'Brien's rebel counterpart and announces he is taking Jake home. Pointing weapons at Sisko, O'Brien replies that neither he nor Jake is going anywhere.
O'Brien tells Sisko they need his help in their fight against the tyrannical Alliance forces. The rebel group built its own Defiant, but is having trouble making the powerful warship operational, and the Alliance is due to attack Terok Nor in four days. Sisko asks to see Jake, who tells his father he came to be with Jennifer. Angry, Sisko takes Jennifer to task for using his son, but still agrees to help. Elsewhere, leading a fleet of Klingon and Cardassian ships, the Alliance Regent, Worf's counterpart, lashes out at Garak's counterpart for losing Terok Nor to the rebels. Garak swears his loyalty as they prepare to take back the station.
Sisko meets up with the counterpart for Kira, once Terok Nor's leader but now a prisoner of the rebels. Meanwhile, Worf learns about the Defiant's construction and increases the fleet's speed to the station. Back on Terok Nor, Jake grows more fond of Jennifer, despite Sisko's concerns, and Jennifer reveals to Sisko that she can't stop thinking of Jake as the son she'll never have. Their moment is interrupted by news that the Alliance fleet is less than eight hours away.
Needing another plan, Sisko asks Kira for help, reminding her that Worf and the Alliance probably blame her for the loss of Terok Nor. Kira tells Sisko that Alliance ships have targeting systems that are easily fooled, information he uses to create a diversion while finishing work on the Defiant. Jennifer assists him and talks about her deepening bond with Jake, then decides to return the child to Deep Space Nine and out of harm's way. The Defiant now ready, Sisko volunteers to lead its rebel crew in battle. Meanwhile, Jennifer prepares to send Jake home. But the pair encounters the evil Kira, who has now escaped and trains her weapon on them.
Kira plans to take Jennifer as a hostage in order to get back into the Regent's good graces — then prepares to fire on Jake. But Jennifer jumps into the line of fire, struck to the ground by the blast. Learning the truth about Jake and Jennifer's connection, Kira spares his life — but promises to collect on this debt later. Back on the Defiant, Sisko, O'Brien and the rebel crew force Worf and the Alliance to retreat after a fierce battle. Sisko returns to Terok Nor, but arrives to find Jake at Jennifer's deathbed. She summons the strength to wish him goodbye, then dies, leaving father and son to deal with her loss a second painful time.